On Sat, Jun 20, 2020, angad sharma wrote:
>
>till here it is okay for one unit of methane but i put 0.1M methane in the
>a box ,and do the following commands then i face the given error.
>
>tleap
>source leaprc.gaff
>loadamberparams meth.frcmod
>loadoff meth.lib
>a = loadpdb meth.pdb
>check a
>saveamberparm a a.prmtop a.inpcrd
Is the "meth.pdb" file used here the same as you used for antechamber?
Does it have just one methane molecule? (Confused because you mentioned
"0.1M" above.)
>
>
>then i get this error
>> check a
>Checking 'a'....
>ERROR: The unperturbed charge of the unit: -0.082000 is not integral.
>WARNING: The unperturbed charge of the unit: -0.082000 is not zero.
>Checking parameters for unit 'a'.
>Checking for bond parameters.
>Checking for angle parameters.
>check: Errors: 1 Warnings: 1
This is not really an error, although it is odd. Look at the charges in
your meth.mol2 or meth.lib file: do they add up to zero? You may need
to manually adjust the charges. But a deviation of 0.082 is really
large, so we need more information, as requested above.
...dac
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Received on Sat Jun 20 2020 - 05:00:03 PDT
